KR norm on raw.cool file

[matteozoia4]

Dear all,

which one would be the standard procedure to assess KR norm on raw.cool file?

Use the "--annotate KR" option or select a specific option with "cooler balance ..."

Many thanks for the help!

M-Z

[Phlya]

Could you clarify what you mean?

Cooler doesn't have KR balancing implemented, but the result of IC procedure it does is the same - except for more stringent filtering of "bad" bins before correction is applied.

[matteozoia4]

Hi, Many thanks for your quick answer. Sorry I am indeed a beginner in Cooler tool usage, and reading through the readthedocs I was unsure of the procedure to apply. Which would then be the command and options to employ in case I would like to pursue with the IC procedure (KR with more stringent filtering) you mentioned ? Many thanks for your time and help, very appreciated! M.Z Zoia Matteo, Ph.D. Student Gene Regulation & Cardiac Development Marco Osterwalder Laboratory Department for BioMedical Research (DBMR) University of Bern Lab 369, Murtenstrasse 28 CH - 3008 Bern SWITZERLAND

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________________________________ Da: Ilya Flyamer ***@***.***> Inviato: domenica, 13. marzo 2022 10:25:24 A: open2c/cooler Cc: Zoia, Matteo (DBMR); Author Oggetto: Re: [open2c/cooler] KR norm on raw.cool file (Discussion #272) Could you clarify what you mean? Cooler doesn't have KR balancing implemented, but the result of IC procedure it does is the same - except for more stringent filtering of "bad" bins before correction is applied. — Reply to this email directly, view it on GitHub<#272 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AUBHT3EFGTWDIK524T7IEW3U7WYAJANCNFSM5QTB44JQ>. Triage notifications on the go with GitHub Mobile for iOS<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[Phlya]

You just use cooler balance <your_file.cool>. Check the additional arguments, in case there is something useful (multiple cores, for example).
In case you want to create a multiresolution cooler by coarsegraining a high resolution file, you can just use cooler zoomify with --balance argument, then very resolution will be balanced too.

[matteozoia4]

Hi, Many thanks for the help and the insights! Both steps are indeed useful! MZ Zoia Matteo, Ph.D. Student Gene Regulation & Cardiac Development Marco Osterwalder Laboratory Department for BioMedical Research (DBMR) University of Bern Lab 369, Murtenstrasse 28 CH - 3008 Bern SWITZERLAND

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________________________________ Da: Ilya Flyamer ***@***.***> Inviato: domenica, 13. marzo 2022 11:06:50 A: open2c/cooler Cc: Zoia, Matteo (DBMR); Author Oggetto: Re: [open2c/cooler] KR norm on raw.cool file (Discussion #272) You just use cooler balance <your_file.cool>. Check the additional arguments, in case there is something useful (multiple cores, for example). In case you want to create a multiresolution cooler by coarsegraining a high resolution file, you can just use cooler zoomify with --balance argument, then very resolution will be balanced too. — Reply to this email directly, view it on GitHub<#272 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AUBHT3FL7MV233DYU5ODXDDU7W43VANCNFSM5QTB44JQ>. Triage notifications on the go with GitHub Mobile for iOS<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you authored the thread.Message ID: ***@***.***>